[R] hclust error

[Adaikalavan Ramasamy]

Herman,

Just out of curiosity, have you tried Mike Eisen's software Cluster
(http://rana.lbl.gov/EisenSoftware.htm). Try version 2.12 instead as
version 2.20 appears to give wrong results.

I never tried with 32000 rows, but when I tried a 10000 row last year it
seem to produce the results in a few minutes whereas R took either too
long or ran out of memory. Let us know if it works.

I assume you are trying to cluster the rows/genes here in which case the
number of columns/samples will not matter in your case.

Regards, Adai.



On Mon, 2004-07-19 at 16:14, Liaw, Andy wrote:
> This has been asked on R-help several times in the past.
> 
> The `dist' object for the data of that size would be:
> 
> > 32513*32512/2
> [1] 528531328
> 
> To store a vector of that size in double precision (8 bytes), you'd need:
> 
> > 32513*32512/2*8/1024^2
> [1] 4032.374
> 
> I.e., that's nearly 4 GB.  Is your computer capable of doing that?
> 
> Andy
> 
> > From: Herman, David (NIH/NIMH)
> > 
> > Hello,
> >             I'm trying to do a cluster analysis on a large 
> > data set.  I
> > tried it out with a smaller one first, but I got this error:
> >  
> > > hc<-hclust(dist(x),"ave")
> > Error: cannot allocate vector of size 4129151 Kb
> >  
> > The data sample used (i.e. "x")  is a numerical data set of 
> > size 32513 by 31
> >  
> > Does anyone know how I can do this analysis?  Is R capable of 
> > this data
> > size?  
> > Ultimately I wanna do an analysis on a dataset of size 32513 by 220
> >  
> >  
> > Thanks!
> >  
> > dave
> >  
> >  
> > 
> > 	[[alternative HTML version deleted]]
> > 
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